def loadEntry(self,
index,
label,
molecule,
thermo,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
molecule = Molecule().fromAdjacencyList(molecule)
# Internal checks for adding entry to the thermo library
if label in self.entries.keys():
raise DatabaseError('Found a duplicate molecule with label {0} in the thermo library. Please correct your library.'.format(label))
for entry in self.entries.values():
if molecule.isIsomorphic(entry.item):
if molecule.multiplicity == entry.item.multiplicity:
raise DatabaseError('Adjacency list and multiplicity of {0} matches that of existing molecule {1} in thermo library. Please correct your library.'.format(label, entry.label))
self.entries[label] = Entry(
index = index,
label = label,
item = molecule,
data = thermo,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def loadEntry(self,
index,
label,
molecule,
thermo,
reference=None,
referenceType='',
shortDesc='',
longDesc='',
):
molecule = Molecule().fromAdjacencyList(molecule)
# Internal checks for adding entry to the thermo library
if label in self.entries.keys():
raise DatabaseError('Found a duplicate molecule with label {0} in the thermo library. Please correct your library.'.format(label))
for entry in self.entries.values():
if molecule.isIsomorphic(entry.item):
raise DatabaseError('Adjacency list of {0} matches that of existing molecule {1} in thermo library. Please correct your library.'.format(label, entry.label))
self.entries[label] = Entry(
index = index,
label = label,
item = molecule,
data = thermo,
reference = reference,
referenceType = referenceType,
shortDesc = shortDesc,
longDesc = longDesc.strip(),
)
def getThermoDataFromDepository(self, species):
"""
Return all possible sets of thermodynamic parameters for a given
:class:`Species` object `species` from the depository. If no
depository is loaded, a :class:`DatabaseError` is raised.
Returns: a list of tuples (thermoData, depository, entry) without any Cp0 or CpInf data.
"""
items = []
for label, entry in self.depository['stable'].entries.iteritems():
for molecule in species.molecule:
if molecule.isIsomorphic(entry.item):
items.append((deepcopy(entry.data), self.depository['stable'], entry))
break
for label, entry in self.depository['radical'].entries.iteritems():
for molecule in species.molecule:
if molecule.isIsomorphic(entry.item):
items.append((deepcopy(entry.data), self.depository['radical'], entry))
break
return items
def getThermoDataFromDepository(self, species):
"""
Return all possible sets of thermodynamic parameters for a given
:class:`Species` object `species` from the depository. If no
depository is loaded, a :class:`DatabaseError` is raised.
Returns: a list of tuples (thermoData, depository, entry) without any Cp0 or CpInf data.
"""
items = []
for label, entry in self.depository['stable'].entries.iteritems():
for molecule in species.molecule:
if molecule.isIsomorphic(entry.item):
items.append((deepcopy(entry.data), self.depository['stable'], entry))
break
for label, entry in self.depository['radical'].entries.iteritems():
for molecule in species.molecule:
if molecule.isIsomorphic(entry.item):
items.append((deepcopy(entry.data), self.depository['radical'], entry))
break
return items
def getThermoDataFromLibrary(self, species, library):
"""
Return the set of thermodynamic parameters corresponding to a given
:class:`Species` object `species` from the specified thermodynamics
`library`. If `library` is a string, the list of libraries is searched
for a library with that name. If no match is found in that library,
``None`` is returned. If no corresponding library is found, a
:class:`DatabaseError` is raised.
Returns a tuple: (ThermoData, library, entry) or None.
"""
for label, entry in library.entries.iteritems():
for molecule in species.molecule:
if molecule.isIsomorphic(entry.item) and entry.data is not None:
thermoData = deepcopy(entry.data)
self.findCp0andCpInf(species, thermoData)
return (thermoData, library, entry)
return None
def getThermoDataFromLibrary(self, species, library):
"""
Return the set of thermodynamic parameters corresponding to a given
:class:`Species` object `species` from the specified thermodynamics
`library`. If `library` is a string, the list of libraries is searched
for a library with that name. If no match is found in that library,
``None`` is returned. If no corresponding library is found, a
:class:`DatabaseError` is raised.
Returns a tuple: (ThermoData, library, entry) or None.
"""
for label, entry in library.entries.iteritems():
for molecule in species.molecule:
if molecule.isIsomorphic(entry.item) and entry.data is not None:
thermoData = deepcopy(entry.data)
self.findCp0andCpInf(species, thermoData)
return (thermoData, library, entry)
return None
